Process_Replication – Replication

Name
WID	Process_Replication
Name	Replication

Implementation
Initialization order	22

Reactions
Chemical reactions	DNA unwinding [c]: ATP + H2O ⇒ ADP + H + PI DNA ligationi [c]: (2) DR5P + NAD ⇒ AMP + dRibose5P_dRibose5P + H + NMN DNA polymerization (dATP) [c]: DAMP + DATP ⇒ dApdAp + PPI DNA polymerization (dCTP) [c]: DCMP + DCTP ⇒ dCpdCp + PPI DNA polymerization (dGTP) [c]: DGMP + DGTP ⇒ dGpdGp + PPI ... 5 more DNA polymerization (dTTP) [c]: DTMP + DTTP ⇒ dTpdTp + PPI DNA primer polymerization (ATP) [c]: AMP + ATP ⇒ ApAp + PPI DNA primer polymerization (CTP) [c]: CMP + CTP ⇒ CpCp + PPI DNA primer polymerization (GTP) [c]: GMP + GTP ⇒ GpGp + PPI DNA primer polymerization (UTP) [c]: UMP + UTP ⇒ PPI + UpUp
Complex formation reactions	DNA polymerase (2) core, β-clamp, γ-complex, and primase [c]: (2) DNA_POLYMERASE_CORE + DNA_POLYMERASE_GAMMA_COMPLEX + (2) MG_001_MONOMER + MG_250_MONOMER ⇒ DNA_POLYMERASE_2CORE_BETA_CLAMP_GAMMA_COMPLEX_PRIMASE DNA polymerase core, β-clamp, and γ-complex [c]: DNA_POLYMERASE_CORE + DNA_POLYMERASE_GAMMA_COMPLEX + (2) MG_001_MONOMER ⇒ DNA_POLYMERASE_CORE_BETA_CLAMP_GAMMA_COMPLEX DNA polymerase core, β-clamp, and primase [c]: DNA_POLYMERASE_CORE + (2) MG_001_MONOMER + MG_250_MONOMER ⇒ DNA_POLYMERASE_CORE_BETA_CLAMP_PRIMASE DNA-directed DNA polymerase holoenzyme [c]: (2) DNA_POLYMERASE_CORE + DNA_POLYMERASE_GAMMA_COMPLEX + (2) MG_001_MONOMER ⇒ DNA_POLYMERASE_HOLOENZYME DNA polymerase III, beta clamp [c]: (2) MG_001_MONOMER ⇒ MG_001_DIMER ... 2 more single-strand binding protein family, octamer [c]: (2) MG_091_TETRAMER ⇒ MG_091_OCTAMER Replisome [c]: (2) DNA_POLYMERASE_CORE + DNA_POLYMERASE_GAMMA_COMPLEX + (4) MG_001_MONOMER + MG_094_HEXAMER + MG_250_MONOMER ⇒ REPLISOME

Parameters
Parameters	Parameter_0109: dnaPolymeraseElongationRate = 100 nt/s Parameter_0110: laggingBackupClampReloadingLength = 750 nt Parameter_0111: ligaseRate = 0.04 1/s Parameter_0112: okazakiFragmentMeanLength = 1500 nt Parameter_0113: primerLength = 11 nt ... 4 more Parameter_0114: ssbComplexSpacing = 30 nt Parameter_0115: startingOkazakiLoopLength = 50 nt Parameter_0145: rnaPolymeraseCollisionMeanDwellTime = 1.7 s Parameter_0152: ssbDissociationRate = 0.3 1/s

Comments
Comments	Summary This function polymerizes DNA bidirectionally from oriC to terC of both the leading and lagging strands. It models the locations of all of the replisome machinery proteins, and applies limits to replication (energy, coordination of strands, availibility of ligases, SSBs,...). References Mirkin, E.V., Mirkin, S.M. (2007). Replication fork stalling at natural impediments. Microbiology and molecular biology reviews 71: 13-35. Mirkin, E.V., Mirkin, S.M. (2005). Mechanisms of Transcription-replication collisions in bacteria. molecular and cellular biology 25: 888-895. Mirkin, E.V., Roa, D.C., Nudler, E., Mirkin, S.M. (2006). Transcription regulatory elements are punctuation marks for dna replication. PNAS 103: 7276-7281. Miyata, M. Cell Division. Molecular biology and pathogenicity of mycoplasmas. Razin, S., Herrmann, R. Kluwer Academic/Plenum Publishers, 2002. 117-130. Rudolph, C.J., Dhillon, P., Moore, T., Lloyd, R.G. (2007). Avoiding and resolving conflicts between DNA replication and transcription. DNA Repair 6: 981-993. McGlynn, P., Guy, C.P. (2008). Replication forks blocked by protein-DNA complexes have limited stability in vitro. J. Mol. Biol. 381: 249-255.

Metadata
Created	2012-10-01 15:07:35
Last updated	2012-10-01 15:14:00